epijenatics.bsky.social
siddhartha jena
@epijenatics.bsky.social
190 followers 560 following 20 posts
buenrostro lab postdoc @ harvard/broad institute. stoked about chromatin, evolution, and bioengineering. sidujena.github.io
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
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philipcball.bsky.social
Philip Ball @philipcball.bsky.social · 10h
I adored writing this piece. It brings together several of the things preoccupying me right now, like chromatin organization and gene regulation. There's so much more to be said on that. Also, these marine critters look gorgeous.
www.quantamagazine.org/loops-of-dna...
Loops of DNA Equipped Ancient Life To Become Complex | Quanta Magazine
New work shows that physical folding of the genome to control genes located far away may have been an early evolutionary development.
www.quantamagazine.org
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Reposted by siddhartha jena
plantevolution.bsky.social
PlantEvolution 🌱🌾 @plantevolution.bsky.social · 1d
Game changer for cell-based plant genetics: the labs of Caixia Gao & Jin-Long Qiu have developed very efficient self-replicating vectors and they just published a very nice proof-of-concept paper.
#plantscience
www.science.org/doi/10.1126/...
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carlbergstrom.com
Carl T. Bergstrom @carlbergstrom.com · 24d
1. What does a Cold War-era game theory problem known as the silent duel have to do with high-risk research strategies, publication in Cell/Nature/Science glamor journals, and the academic job market?

Kevin Gross and I tackle these questions in our latest arXiv preprint: arxiv.org/abs/2509.06718
How competition propels scientific risk-taking Kevin Gross∗ Department of Statistics North Carolina State University Raleigh, NC USA Carl T. Bergstrom† Department of Biology University of Washington Seattle, WA USA (Dated: September 9, 2025) In science as elsewhere, attention is a limited resource and scientists compete with one another to produce the most exciting, novel and impactful results. We develop a game-theoretic model to explore how such competition influences the degree of risk that scientists are willing to embrace in their research endeavors. We find that competition for scarce resources—for example, publications in elite journals, prestigious prizes, and faculty jobs—motivates scientific risk-taking and may be important in counterbalancing other incentives that favor cautious, incremental science. Even small amounts of competition induce substantial risk-taking. Moreover, we find that in an “opt-in” contest, increasing the stakes induces increased participation—which crowds the contest and further impels entrants to pursue higher-risk, higher-return investigations. The model also illuminates a source of tension in academic training and collaboration. Researchers at different career stages differ in their need to amass accomplishments that distinguish them from their peers, and therefore may not agree on what degree of risk to accept.
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 14d
This is a great initiative, and would be an invaluable resource to learn more about (and maybe borrow from!) the diversity of cellular organization and regulation across evolution!
arnausebe.bsky.social
Arnau Sebé-Pedrós @arnausebe.bsky.social · 14d
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 15d
very cool image-based screening of HP1 condensates and implications for RNA in regulating mesoscale structures!
serenasanulli.bsky.social
Serena Sanulli Lab at Stanford Genetics @serenasanulli.bsky.social · 16d
Excited to share our first preprint! We developed an image-based pooled screen to uncover regulators of HP1 condensates and discovered a link with intronic RNA and RNA processing. 👏 Congrats to all authors, especially Matthew, Shaopu & Chris!
biorxiv-genetic.bsky.social
bioRxiv Genetics @biorxiv-genetic.bsky.social · 16d
An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates https://www.biorxiv.org/content/10.1101/2025.09.21.676939v1
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Reposted by siddhartha jena
andersshansen.bsky.social
Anders Sejr Hansen @andersshansen.bsky.social · 17d
Asking BlueSky for help: For a review, I am trying to accurately credit the first paper that measured pairwise 3D distances between 2 pieces of DNA on the same chromosome (or cosmid). Is Trask 1989 the first?
I know of earlier single-locus papers (1982).
www.sciencedirect.com/science/arti...
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Reposted by siddhartha jena
sedonamurphy.bsky.social
Dr. Sedona Murphy @sedonamurphy.bsky.social · 19d
Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...
Kinetic organization of the genome revealed by ultraresolution multiscale live imaging
Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...
www.science.org
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biorxiv-synthbio.bsky.social
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 27d
Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Thank you Kaushik!
epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
It’d be so cool to screen evolutionarily divergent CENP-A and map effects on centromere organization!
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Thank you!
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Thank you so much!
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
One last thing - I am on the job market! My lab will extend this approach to decode resilient chromatin: adaptations in proteins/DNA that allow for survival in harsh environments. These hold the 🔑 to designing cells that thrive under stress, esp. as we push the limits of where we take them ❄️🚀🪐🌱9/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Huge thanks to all co-authors and the inimitable @jbuenrostro.bsky.social for supporting this new direction - I got to think about evolution, engineering, chromatin biophysics, and modeling during the course of this project. For more, check out the preprint: www.biorxiv.org/content/10.1... 8/9
Engineered histones reshape chromatin in human cells
Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between ...
www.biorxiv.org
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
This work is a proof of concept towards fully programmable chromatin, something I think will become very common. By combining evolutionary insights, high-throughput assays and predictive/generative modeling, we should be able to uncover some true “superpowers” of chromatin (more on this soon!) 7/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Finally, we set out to achieve what I’d always wanted. Using screen data and sequence embeddings, we trained a classifier to predict heterochromatin repression, and used it to design totally synthetic histones we called synH4s that demonstrate optimized heterochromatin-repressing activity. 6/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
This process was able to alter cellular plasticity to transcription factor inputs: T cells expressing the tail mutant G4D displayed increased accessibility of heterochromatin-associated transcription factors and were able to respond to overexpression of those factors with proliferation! 5/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
We were surprised to see that some mutations in the N-terminal tail of H4 caused outsized effects on chromatin structure- digging in deeper, we found that these mutations alter nucleosomes in cis, ablating the heterochromatin mark H3K9me3 and shaping spatial compartmentalization in the nucleus. 4/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
The first step was defining sequence-to-function relationships. To do this, we turned to high-throughput screening of 1000s of variants for effects on chromatin accessibility and histone marks. We found that some single-residue changes have global effects on chromatin structure! 3/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Organisms across the tree of life, including humans, have evolved histone sequences that remodel chromatin in diverse ways. As I learned about these examples, I grew mildly obsessed with the idea of designing histones to do what *I* wanted them to do. 2/9
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epijenatics.bsky.social
siddhartha jena @epijenatics.bsky.social · 27d
Excited to share my postdoc work, out on bioRxiv today! Histones package DNA into nucleosomes to form the building blocks of chromatin, but how modular and programmable is this system? 1/9
1 32 82
Reposted by siddhartha jena
mokhalil.bsky.social
Mo Khalil @mokhalil.bsky.social · Jul 21
We traveled to DC to talk to Congressional Staffers about the impact of NIH and NIBIB funding. It enables us to develop synthetic biology tools to advance cell & genetic medicines for patients in need. REPOST to deliver the message that SCIENCE saves lives & makes America GREAT!
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Reposted by siddhartha jena
streets.boston.gov
City of Boston Streets Cabinet @streets.boston.gov · Jul 14
What'd you do over the weekend? Public Works began resurfacing the street in front of the Chipotle where Thomas Paine wrote Common Sense
Boston Public Works Department crews raising castings on School Street
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Reposted by siddhartha jena
letterboxd.social
Letterboxd @letterboxd.social · Jul 13
spending the day watching movies isn’t procrastination, it’s leveling up your cinephile game😎
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Reposted by siddhartha jena
ruthfranklinlab.bsky.social
Ruth Franklin @ruthfranklinlab.bsky.social · Jul 11
🎉 Over the moon to share the first paper from my lab!! We discovered an unexpected role for the cytokine OSM in lung epithelial homeostasis and repair. 🧵 1/n www.science.org/doi/10.1126/...
Macrophage-derived oncostatin M repairs the lung epithelial barrier during inflammatory damage
Tissue repair programs must function alongside antiviral immunity to restore the lung epithelial barrier following infection. We found that macrophage-derived oncostatin M (OSM) counteracted the patho...
www.science.org
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